--- a/mafft.xml	Thu Jun 18 08:59:56 2015 -0400
+++ b/mafft.xml	Fri Jul 31 19:02:11 2015 -0400
@@ -42,6 +42,7 @@
         <conditional name="cond_flavour">
             <param name="flavourType" type="select" label="MAFFT flavour" help="Run mafft with pre-defined input parameters. Specification of these parameters can be found in the help section.">
                 <option value="mafft-fftns" selected="true">fftns</option>
+                <option value="mafft --auto">auto</option>
                 <option value="mafft-fftnsi">fftnsi</option>
                 <option value="mafft-nwns">nwns</option>
                 <option value="mafft-nwnsi">nwnsi</option>
@@ -53,6 +54,7 @@
                 <!-- <option value="custom">Custom Parameters</option> this should trigger tweaking of all parameters -->
             </param>
             <when value="mafft-fftns"/>
+            <when value="mafft --auto"/>
             <when value="mafft-fftnsi"/>
             <when value="mafft-nwns"/>
             <when value="mafft-nwnsi"/>
@@ -143,7 +145,11 @@
 - NW-NS-PartTree-1 (recommended for ~10,000 to ~50,000 sequences; progressive method with the PartTree algorithm):
 
     - mafft --retree 1 --maxiterate 0 --nofft --parttree input [> output]
-    
+
+**Options:**
+
+--auto
+    Automatically selects an appropriate strategy from L-INS-i, FFT-NS-i and FFT-NS-2, according to data size. Default: off (always FFT-NS-2)
     ]]>
     </help>
     <citations>